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Characterization of maize B-chromosome-related transcripts isolated via cDNA-AFLP

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Abstract

The maize B-chromosome consists mainly of heterochromatin and is considered to be genetically inert. However, the B-chromosome contains euchromatin that carries control elements that direct its behaviors during cell division, such as nondisjunction during the second pollen mitosis. To determine the transcriptional activity of the B-chromosome, complementary DNA-amplified fragment length polymorphism analysis was applied to five inbred maize lines with and without B-chromosomes. Six putative B-chromosome-related transcripts were identified, four of which were cloned and characterized via Southern hybridization, fluorescence in situ hybridization, and sequence comparison to further confirm their B-chromosome origin. All the analyzed B-chromosome-related transcript sequences were repetitive and showed homology to A-chromosomes. Quantitative real-time reverse transcriptase-polymerase chain reaction revealed that the B-chromosome-specific transcribed sequences B3547-179 and B3849-212 were transcribed in a B-chromosome-dosage-dependent manner. Expression of B3849-189 and B3849-147 was not specific to the B-chromosome; however, the former showed a transcriptional pattern with B-chromosome dosage compensation, and the latter displayed down-regulation of transcription due to higher B-chromosome numbers. Using four B-10L translocations, B3849-212 was mapped to the B-chromosome region that contains the nondisjunction control elements of the B-chromosome. Taken together, our results suggested that the maize B-chromosome harbors few transcriptionally active sequences and might influence the transcription of A-chromosomes.

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Acknowledgments

This work was supported by the National Sciences Council grant of Taiwan (NSC99-2311-B-005-003-MY3 and NSC102-2311-B-005-001-).

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Authors and Affiliations

  1. Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan

    Huan-Zhi Lin, Chien-Yu Lin & Ya-Ming Cheng

  2. Department of Medical Research, China Medical University Hospital, Taichung, Taiwan

    Wei-De Lin

  3. School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan

    Wei-De Lin

  4. Department of Biological Science and Technology, China Medical University, Taichung, Taiwan

    Shu-Fen Peng

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  1. Huan-Zhi Lin
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  2. Wei-De Lin
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Correspondence to Ya-Ming Cheng.

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Supplementary Figure 1

B-chromosome breakpoints and chromosome compositions of four B-10L translocations. (a) The figure was modified from Cheng and Lin (2003). BS, B-chromosome short arm; CK, B-centromere and centromeric knob; PE, proximal euchromatin; DH1-DH4, four distal heterochromatins; DE, distal euchromatin. (b) A translocation heterozygote contains 10, 10-B, and B-10 chromosomes; a tertiary trisomy includes 10, 10, B-10 chromosomes; and a hypoploid carries 10 and 10-B chromosomes. Breakpoints of the B-chromosome are indicated as arrows, and arrowheads indicate the centromeres of chromosome 10 or B-chromosome (GIF 211 kb)

High resolution image (TIFF 725 kb)

Supplementary Figure 2

Comparison of maize B73 genome sequences and four +1B-related transcripts. Black thin lines represent sequences of the four +1B-related transcripts. Gray arrows indicate the region that shows the highest identity with sequences in the maize B73 inbred line genome database (B73 RefGen_V2 in the MaizeGDB database). The numbers of B73 sequences that have at least 80% identity with the +1B-related transcript are indicated (GIF 37 kb)

High resolution image (TIFF 43 kb)

Supplementary Figure 3

Southern hybridization of four +1B-related transcripts. Genomic DNA of L289+0B (0B), L289+1B (1B), and L289+9B (9B) was digested with EcoRI, HindIII, BamHI, XbaI, and SacI, and then hybridized with the four +1B-related transcripts B3547-179 (a), B3849-147 (b), B3849-189 (c), and B3849-212(d), respectively. The hollow arrow is representative of B-specific signals, and the solid arrow is representative of signals with B-dosage dependency following the numbers of B-chromosomes. Molecular weights are marked on left (GIF 2771 kb)

High resolution image (TIFF 2510 kb)

Supplementary Figure 4

RT-PCR primers designation of four +1B-related transcripts. Sequences of B3547-179 (a), B3849-147 (b), B3849-189 (c), and 3849–212 (d) were aligned with their top ten homologous sequences in the maize B73 inbred line genome database (B73 RefGen_V2 in the MaizeGDB database). The consensus sequences are highlight in black, and RT-PCR primer binding sites are marked by arrows (GIF 1954 kb)

High resolution image (TIFF 6957 kb)

Supplementary Figure 5

Alignment of genomic and transcribed sequences of three +1B-related transcripts. PCR products of B3849-212 (a), B3849-147 (b), and B3849-189 (c) amplified from genomic DNA (L289+0B, L289+1B, and L289+6B) and cDNA (L289+0B, L289+1B, and L289+9B) were cloned, sequenced, and aligned with their corresponding +1B-related transcript sequences. Conserved nucleotides are shaded with gray and black (GIF 4616 kb)

(GIF 4589 kb)

(GIF 7338 kb)

High resolution image (TIFF 1701 kb)

High resolution image (TIFF 1555 kb)

High resolution image (TIFF 2822 kb)

Supplementary Table 1

(DOC 60 kb)

Supplementary Table 2

(DOC 38 kb)

Supplementary Table 3

(DOC 86 kb)

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Lin, HZ., Lin, WD., Lin, CY. et al. Characterization of maize B-chromosome-related transcripts isolated via cDNA-AFLP. Chromosoma 123, 597–607 (2014). https://doi.org/10.1007/s00412-014-0476-7

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  • DOI: https://doi.org/10.1007/s00412-014-0476-7

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